Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008487.1 Corchorus capsularis cultivar CVL-1 contig08508, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2220
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:755 original size:37 final size:38
Alignment explanation
Indices: 709--787 Score: 151
Period size: 37 Copynumber: 2.1 Consensus size: 38
699 AGATTTTTCC
709 TCAATTTCCGGCCAAAATACTCATAAAAAATATATAGT
1 TCAATTTCCGGCCAAAATACTCATAAAAAATATATAGT
747 TCAA-TTCCGGCCAAAATACTCATAAAAAATATATAGT
1 TCAATTTCCGGCCAAAATACTCATAAAAAATATATAGT
784 TCAA
1 TCAA
788 CTCTAAAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
37 37 0.90
38 4 0.10
ACGTcount: A:0.46, C:0.19, G:0.08, T:0.28
Consensus pattern (38 bp):
TCAATTTCCGGCCAAAATACTCATAAAAAATATATAGT
Found at i:1072 original size:369 final size:372
Alignment explanation
Indices: 385--1113 Score: 938
Period size: 369 Copynumber: 2.0 Consensus size: 372
375 AATTTCTGGA
* * * *
385 CAAAATATTCTTAAAAAATGTATAATTCAACTCTAAAAAAATCGAAGCGCATTTCATGCCTCTAA
1 CAAAATACTCATAAAAAATATATAATTCAACTCTAAAAAAAGCGAAGCGCATTTCATGCCTCTAA
* * * * * *
450 TATCATTTTCTTCTAATTTTTTTTCCGAATTAATATCTACTTAAATCGAAATAAGATTCAGATAC
66 TATCATTTTCTTCTAATTTTTTTCCCGAAATAATATCGAATT-AATCGAAACAAAATTCAGATAC
* * * * * * *
515 TCGTAAAAACAAATCCTTCATTGCGATGTGGCTGAGATTTGTTTAGATGAGTATGGGTATTTCAA
130 TCATAAAAACAAATCCTTAATTGCAATGTGGCTGAGATTTGTTTAGATCAATATAGATATTTCAA
* *
580 GGATGCTTGGCGCCAAAAATCGAGAAAAATATGCCGGGTCCTCGGAACGCGTTTTTTTGCCAAAA
195 GGATGCTTGGCGCCAAAAATCAAGAAAAATATGCCGGGTCCTCGGAACGCGTTTTTTAGCCAAAA
* * *
645 ATCGTGATTTATACTACACGATTTCAGTTAAAATTTTGCCAAAATTGACCCAAAAGATTTTTCCT
260 ACCGTGATGTATACTACACGATTTCAGTTAAAATTTTGCAAAAATTGACCCAAAAGATTTTTCCT
710 CAATTTCCGGCCAAAATACTCATAAAAAATATATAGTTCAATTCCGGC
325 CAATTTCCGGCCAAAATACTCATAAAAAATATATAGTTCAATTCCGGC
* * * * * *
758 CAAAATACTCATAAAAAATATATAGTTCAACTCTAAAAATAGCGAAGGGCTTTTCATGCTTCTGA
1 CAAAATACTCATAAAAAATATATAATTCAACTCTAAAAAAAGCGAAGCGCATTTCATGCCTCTAA
*
823 TATCATTTT-TTCT-ATTTTTTTCCCGAAATAACT-TCGAATT-ATCGAAACAAAATTCAGATGC
66 TATCATTTTCTTCTAATTTTTTTCCCGAAATAA-TATCGAATTAATCGAAACAAAATTCAGATAC
*
884 TCATAAAAACAAATCCTTAATTGCAATGT-GCTTGAGATTTTTTTAGATCAATATAGATA-TTCT
130 TCATAAAAACAAATCCTTAATTGCAATGTGGC-TGAGATTTGTTTAGATCAATATAGATATTTC-
* *
947 AAGGA-GTCTTGGCGCCAAAAATCAAGCAAAACTTATG-CGGGTCC-CGGAACGCGTTTTTTAGT
193 AAGGATG-CTTGGCGCCAAAAATCAAG-AAAA-ATATGCCGGGTCCTCGGAACGCGTTTTTTAGC
* * * * *
1009 CAAAAACCGTGATGGT-TAGTACATGATTTCAGTTATAATTTTGCAAAAATTGACTCGAAAGATT
255 CAAAAACCGTGAT-GTATACTACACGATTTCAGTTAAAATTTTGCAAAAATTGACCCAAAAGATT
** * * *
1073 TTTCCTCAATTTTTGGTCAAAATATTCATAAAAAATGTATA
319 TTTCCTCAATTTCCGGCCAAAATACTCATAAAAAATATATA
1114 ATTTAACTCT
Statistics
Matches: 307, Mismatches: 42, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
368 6 0.02
369 195 0.64
370 12 0.04
371 25 0.08
372 5 0.02
373 64 0.21
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (372 bp):
CAAAATACTCATAAAAAATATATAATTCAACTCTAAAAAAAGCGAAGCGCATTTCATGCCTCTAA
TATCATTTTCTTCTAATTTTTTTCCCGAAATAATATCGAATTAATCGAAACAAAATTCAGATACT
CATAAAAACAAATCCTTAATTGCAATGTGGCTGAGATTTGTTTAGATCAATATAGATATTTCAAG
GATGCTTGGCGCCAAAAATCAAGAAAAATATGCCGGGTCCTCGGAACGCGTTTTTTAGCCAAAAA
CCGTGATGTATACTACACGATTTCAGTTAAAATTTTGCAAAAATTGACCCAAAAGATTTTTCCTC
AATTTCCGGCCAAAATACTCATAAAAAATATATAGTTCAATTCCGGC
Found at i:1897 original size:333 final size:333
Alignment explanation
Indices: 758--2220 Score: 2225
Period size: 332 Copynumber: 4.4 Consensus size: 333
748 CAATTCCGGC
* * * *
758 CAAAATACTCATAAAAAATATATAGTTCAACTCTAAAAATAGCGAAGGGCT-TTTCATGCTTCTG
1 CAAAATATTCATAAAAAATATATAATTCAACTCTAAAAATATCGAAGGG-TGTTTCATGCTTCTA
* * *
822 ATATCATTTTTTCT-ATTTTTTTCCCGAAATAACTTCGAATT--ATCGAAACAAAATTCAGATGC
65 ATATCATTTTTTCTAATTTTTTT-CCGAATTAATTTCGAATTAAATCGAAACAAGATTCAGATGC
*
884 TCATAAAAACAAATCCTTAATTGCAATGTGCTTGAGATTTTTTTAGATCAATATAGATA-TTCTA
129 TCATAAAAACAAATCCTTAATTGCAATGTGCCTGAGATTTTTTTAGATCAATATAGATATTTC-A
** * *
948 AGGAGTCTTGGCGCCAAAAATCAAGCAAAACTTATGCGGGT-CCCGGAACGCGTTTTTTAGTCAA
193 AGGAGTCTTGGCGCCAAAAATCAAGCAAAACCGAGGCGGGTCCCCGGAACGCGTTTTTT-GCCAA
* * *
1012 AAACCGTGATGGTTAGTACATGATTTCAGTTATAATTTTGCAAAAATTGACTCGAAAGATTTTTC
257 AAACCGTGATGGTTAGTACACGATTTCAGTTAAAATTTTGCAAAAATTGAC-CGAAAGATCTTTC
1077 CTCAATTTTTGGT
321 CTCAATTTTTGGT
* * *
1090 CAAAATATTCATAAAAAATGTATAATTTAACTCTAAAAATATCGAAGTGTGTTTCATGCTTCTAA
1 CAAAATATTCATAAAAAATATATAATTCAACTCTAAAAATATCGAAGGGTGTTTCATGCTTCTAA
* * *
1155 TATCATTTTTTCTAATTTTTTTCTGAATTAATTTCGAATTAAATCGAAAGAAGATTCAGATGCGC
66 TATCATTTTTTCTAATTTTTTTCCGAATTAATTTCGAATTAAATCGAAACAAGATTCAGATGCTC
* * *
1220 ATAAAAACAAATCCTCAATTGCCATGTGCCTGAGATTTGTTTAGATCAATATAGATATTTCAAGG
131 ATAAAAACAAATCCTTAATTGCAATGTGCCTGAGATTTTTTTAGATCAATATAGATATTTCAAGG
* * * * ** *
1285 AATCTTAGTGCCAAAAATCAAGCAAAACCGAGTCGGGTCCCCGGAAATCG-TTTTTGTCAAAAAC
196 AGTCTTGGCGCCAAAAATCAAGCAAAACCGAGGCGGGTCCCCGGAACGCGTTTTTTGCCAAAAAC
* *
1349 CGTGATGGTTAGTACATGATTTCAGTTAAAATTTTGCAAAAGTTGACCGAAAGATCTTTCCTCAA
261 CGTGATGGTTAGTACACGATTTCAGTTAAAATTTTGCAAAAATTGACCGAAAGATCTTTCCTCAA
*
1414 TTTTTGGA
326 TTTTTGGT
*
1422 CAAAATATTCCTAAAAAATATATAATTCAACTCTAAAAATATCGAAGGGTGTTTCATGCTTCTAA
1 CAAAATATTCATAAAAAATATATAATTCAACTCTAAAAATATCGAAGGGTGTTTCATGCTTCTAA
*
1487 TATCATTTTTTCTAATTTTTTTCCTAATTAATTTCGAATTAAATCGAAACAAGATTCAGATGCTC
66 TATCATTTTTTCTAATTTTTTTCCGAATTAATTTCGAATTAAATCGAAACAAGATTCAGATGCTC
1552 ATAAAAACAAATCCTTAATTGCAATGTGCCTGAGATTTTTTTAGATCAATATAGATATTTCAAGG
131 ATAAAAACAAATCCTTAATTGCAATGTGCCTGAGATTTTTTTAGATCAATATAGATATTTCAAGG
*
1617 AGTCTTGGCGCCAAAAATCAAGCAAAACCGAGGCGGGTCCCCGGAATGCGTTTTTTGCCAAAAAC
196 AGTCTTGGCGCCAAAAATCAAGCAAAACCGAGGCGGGTCCCCGGAACGCGTTTTTTGCCAAAAAC
*
1682 CGTGATGGTTAGTACACGATTTCAGTTAAAATTTCTGCAAAAATTGACCCGAAAGATTTTTCCTC
261 CGTGATGGTTAGTACACGATTTCAGTTAAAATTT-TGCAAAAATTGA-CCGAAAGATCTTTCCTC
1747 AATTTTTGGT
324 AATTTTTGGT
*
1757 CAAAATATTCAT-AAAAATGTATAATTCAACTCTAAAAATATCGAAGGGTGTTTCATGCTTCTAA
1 CAAAATATTCATAAAAAATATATAATTCAACTCTAAAAATATCGAAGGGTGTTTCATGCTTCTAA
1821 TATCATTTTTTCTAA-TTTTTTCCGAATTAATTTCGAATTAAATCGAAACAAGATTCAGATGCTC
66 TATCATTTTTTCTAATTTTTTTCCGAATTAATTTCGAATTAAATCGAAACAAGATTCAGATGCTC
1885 ATAAAAACAAATCCTTAATTGCAATGTGCCTGAGA-TTTTTTAGATCAATATAGATATTTCAAGG
131 ATAAAAACAAATCCTTAATTGCAATGTGCCTGAGATTTTTTTAGATCAATATAGATATTTCAAGG
* ** *
1949 AGTCTTGGCGCCAAAAATAAAGCAAAACCGAGTTGGGTCCCTGGAACGCGTTTTTTTGCCAAAAA
196 AGTCTTGGCGCCAAAAATCAAGCAAAACCGAGGCGGGTCCCCGGAACGCG-TTTTTTGCCAAAAA
** *
2014 CCGTGATGGTTAGTACACGATTTCAGTTAAAATTTTGCAAATGTTGACCGAAAGATCTTTGCTCA
260 CCGTGATGGTTAGTACACGATTTCAGTTAAAATTTTGCAAAAATTGACCGAAAGATCTTTCCTCA
2079 ATTTTTGG-
325 ATTTTTGGT
* * *
2087 ------------AAAAAATATATACTTCAACTCTTAAAATATCGAAGGTTGTTTCAATGCTTCTA
1 CAAAATATTCATAAAAAATATATAATTCAACTCTAAAAATATCGAAGGGTGTTTC-ATGCTTCTA
*
2140 ATATCATTTTTTCTAAATTTTTTTCCGAATTAATTTCGAATTAAATCGAAATAAGATTCAGATGC
65 ATATCATTTTTTCT-AATTTTTTTCCGAATTAATTTCGAATTAAATCGAAACAAGATTCAGATGC
2205 TCATAAAAACAAATCC
129 TCATAAAAACAAATCC
Statistics
Matches: 1048, Mismatches: 69, Indels: 38
0.91 0.06 0.03
Matches are distributed among these distances:
319 38 0.04
320 23 0.02
321 2 0.00
322 62 0.06
331 25 0.02
332 420 0.40
333 240 0.23
334 190 0.18
335 48 0.05
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Consensus pattern (333 bp):
CAAAATATTCATAAAAAATATATAATTCAACTCTAAAAATATCGAAGGGTGTTTCATGCTTCTAA
TATCATTTTTTCTAATTTTTTTCCGAATTAATTTCGAATTAAATCGAAACAAGATTCAGATGCTC
ATAAAAACAAATCCTTAATTGCAATGTGCCTGAGATTTTTTTAGATCAATATAGATATTTCAAGG
AGTCTTGGCGCCAAAAATCAAGCAAAACCGAGGCGGGTCCCCGGAACGCGTTTTTTGCCAAAAAC
CGTGATGGTTAGTACACGATTTCAGTTAAAATTTTGCAAAAATTGACCGAAAGATCTTTCCTCAA
TTTTTGGT
Found at i:2027 original size:666 final size:663
Alignment explanation
Indices: 758--2220 Score: 2316
Period size: 666 Copynumber: 2.2 Consensus size: 663
748 CAATTCCGGC
* * *
758 CAAAATACTCATAAAAAATATATAGTTCAACTCTAAAAATAGCGAAGGGCT-TTTCATGCTTCTG
1 CAAAATA-TC-TAAAAAATATATAATTCAACTCTAAAAATATCGAAGGG-TGTTTCATGCTTCTA
* * *
822 ATATCATTTTTTCT-ATTTTTTTCCCGAAATAACTTCGAATT--ATCGAAACAAAATTCAGATGC
63 ATATCATTTTTTCTAATTTTTTT-CCGAATTAATTTCGAATTAAATCGAAACAAGATTCAGATGC
*
884 TCATAAAAACAAATCCTTAATTGCAATGTGCTTGAGATTTTTTTAGATCAATATAGATATTCTAA
127 TCATAAAAACAAATCCTTAATTGCAATGTGCCTGAGATTTTTTTAGATCAATATAGATATTCTAA
** * *
949 GGAGTCTTGGCGCCAAAAATCAAGCAAAACTTATGCGGGTCCCGGAACGCGTTTTTTAGTCAAAA
192 GGAGTCTTGGCGCCAAAAATCAAGCAAAACCGAGGCGGGTCCCGGAACGCGTTTTTTAGCCAAAA
* * *
1014 ACCGTGATGGTTAGTACATGATTTCAGTTATAATTTTGCAAAAATTGACTCGAAAGATTTTTCCT
257 ACCGTGATGGTTAGTACACGATTTCAGTTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCT
* *
1079 CAATTTTTGGTCAAAATATTCATAAAAAATGTATAATTTAACTCTAAAAATATCGAAGTGTGTTT
322 CAATTTTTGGTCAAAATATTCATAAAAAATGTATAATTCAACTCTAAAAATATCGAAGGGTGTTT
* *
1144 CATGCTTCTAATATCATTTTTTCTAATTTTTTTCTGAATTAATTTCGAATTAAATCGAAAGAAGA
387 CATGCTTCTAATATCATTTTTTCTAATTTTTTTCCGAATTAATTTCGAATTAAATCGAAACAAGA
*
1209 TTCAGATGCGCATAAAAACAAATCCTCAATTGCCATGTGCCTGAGATTTGTTTAGATCAATATAG
452 TTCAGATGCGCATAAAAACAAATCCTCAATTGCAATGTGCCTGAGATTTGTTTAGATCAATATAG
* * *
1274 ATATTTCAAGGAATCTTAGTGCCAAAAATCAAGCAAAACCGAGTCGGGTCCCCGGAAATCGTTTT
517 ATATTTCAAGGAATCTTAGCGCCAAAAATAAAGCAAAACCGAGTCGGGTCCCCGGAAAGCGTTTT
* *
1339 TGTCAAAAACCGTGATGGTTAGTACATGATTTCAGTTAAAATTTTGCAAAAGTTGACCGAAAGAT
582 TGCCAAAAACCGTGATGGTTAGTACACGATTTCAGTTAAAATTTTGCAAAAGTTGACCGAAAGAT
1404 CTTTCCTCAATTTTTGG
647 CTTTCCTCAATTTTTGG
1421 ACAAAATATTCCTAAAAAATATATAATTCAACTCTAAAAATATCGAAGGGTGTTTCATGCTTCTA
1 -CAAAATA-T-CTAAAAAATATATAATTCAACTCTAAAAATATCGAAGGGTGTTTCATGCTTCTA
*
1486 ATATCATTTTTTCTAATTTTTTTCCTAATTAATTTCGAATTAAATCGAAACAAGATTCAGATGCT
63 ATATCATTTTTTCTAATTTTTTTCCGAATTAATTTCGAATTAAATCGAAACAAGATTCAGATGCT
1551 CATAAAAACAAATCCTTAATTGCAATGTGCCTGAGATTTTTTTAGATCAATATAGATATT-TCAA
128 CATAAAAACAAATCCTTAATTGCAATGTGCCTGAGATTTTTTTAGATCAATATAGATATTCT-AA
*
1615 GGAGTCTTGGCGCCAAAAATCAAGCAAAACCGAGGCGGGTCCCCGGAATGCGTTTTTT-GCCAAA
192 GGAGTCTTGGCGCCAAAAATCAAGCAAAACCGAGGCGGGT-CCCGGAACGCGTTTTTTAGCCAAA
1679 AACCGTGATGGTTAGTACACGATTTCAGTTAAAATTTCTGCAAAAATTGACCCGAAAGATTTTTC
256 AACCGTGATGGTTAGTACACGATTTCAGTTAAAATTT-TGCAAAAATTGACCCGAAAGATTTTTC
1744 CTCAATTTTTGGTCAAAATATTCAT-AAAAATGTATAATTCAACTCTAAAAATATCGAAGGGTGT
320 CTCAATTTTTGGTCAAAATATTCATAAAAAATGTATAATTCAACTCTAAAAATATCGAAGGGTGT
1808 TTCATGCTTCTAATATCATTTTTTCTAA-TTTTTTCCGAATTAATTTCGAATTAAATCGAAACAA
385 TTCATGCTTCTAATATCATTTTTTCTAATTTTTTTCCGAATTAATTTCGAATTAAATCGAAACAA
* *
1872 GATTCAGATGCTCATAAAAACAAATCCTTAATTGCAATGTGCCTGAGATTT-TTTAGATCAATAT
450 GATTCAGATGCGCATAAAAACAAATCCTCAATTGCAATGTGCCTGAGATTTGTTTAGATCAATAT
* * * * *
1936 AGATATTTCAAGGAGTCTTGGCGCCAAAAATAAAGCAAAACCGAGTTGGGTCCCTGGAACGCGTT
515 AGATATTTCAAGGAATCTTAGCGCCAAAAATAAAGCAAAACCGAGTCGGGTCCCCGGAAAGCG--
*
2001 TTTTTGCCAAAAACCGTGATGGTTAGTACACGATTTCAGTTAAAATTTTGCAAATGTTGACCGAA
578 TTTTTGCCAAAAACCGTGATGGTTAGTACACGATTTCAGTTAAAATTTTGCAAAAGTTGACCGAA
*
2066 AGATCTTTGCTCAATTTTTGG
643 AGATCTTTCCTCAATTTTTGG
* * *
2087 ----------AAAAAATATATACTTCAACTCTTAAAATATCGAAGGTTGTTTCAATGCTTCTAAT
1 CAAAATATCTAAAAAATATATAATTCAACTCTAAAAATATCGAAGGGTGTTTC-ATGCTTCTAAT
*
2142 ATCATTTTTTCTAAATTTTTTTCCGAATTAATTTCGAATTAAATCGAAATAAGATTCAGATGCTC
65 ATCATTTTTTCT-AATTTTTTTCCGAATTAATTTCGAATTAAATCGAAACAAGATTCAGATGCTC
2207 ATAAAAACAAATCC
129 ATAAAAACAAATCC
Statistics
Matches: 746, Mismatches: 41, Indels: 33
0.91 0.05 0.04
Matches are distributed among these distances:
653 40 0.05
654 23 0.03
655 64 0.09
663 1 0.00
664 153 0.21
665 92 0.12
666 306 0.41
667 67 0.09
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Consensus pattern (663 bp):
CAAAATATCTAAAAAATATATAATTCAACTCTAAAAATATCGAAGGGTGTTTCATGCTTCTAATA
TCATTTTTTCTAATTTTTTTCCGAATTAATTTCGAATTAAATCGAAACAAGATTCAGATGCTCAT
AAAAACAAATCCTTAATTGCAATGTGCCTGAGATTTTTTTAGATCAATATAGATATTCTAAGGAG
TCTTGGCGCCAAAAATCAAGCAAAACCGAGGCGGGTCCCGGAACGCGTTTTTTAGCCAAAAACCG
TGATGGTTAGTACACGATTTCAGTTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAAT
TTTTGGTCAAAATATTCATAAAAAATGTATAATTCAACTCTAAAAATATCGAAGGGTGTTTCATG
CTTCTAATATCATTTTTTCTAATTTTTTTCCGAATTAATTTCGAATTAAATCGAAACAAGATTCA
GATGCGCATAAAAACAAATCCTCAATTGCAATGTGCCTGAGATTTGTTTAGATCAATATAGATAT
TTCAAGGAATCTTAGCGCCAAAAATAAAGCAAAACCGAGTCGGGTCCCCGGAAAGCGTTTTTGCC
AAAAACCGTGATGGTTAGTACACGATTTCAGTTAAAATTTTGCAAAAGTTGACCGAAAGATCTTT
CCTCAATTTTTGG
Done.